Modified dna quadruplex-forming oligonucleotides and methods of use

Abstract

Oligonucleotides according to the following Formula I are provided herein: 5′-X a -Q-Y b -3′ wherein X and Y are each independently selected from the group consisting of a lipid and a polyethylene glycol; Q is a quadruplex-forming guanine-rich promoter gene oligonucleotide (GPGO); a is 0 or 1; and b is 0 or 1, wherein the sum of a+b=1 or 2. Also provided are compositions including Formula I oligonucleotides and methods of their use in inhibiting cell growth, treating cancer, and treating tumors.

1 . An oligonucleotide according to the following Formula I:
   5′-X a -Q-Y b -3′   Formula I
   wherein:   X and Y are each independently selected from the group consisting of a lipid and a polyethylene glycol;   Q is a quadruplex-forming guanine-rich promoter gene oligonucleotide (GPGO);   a is 0 or 1; and   b is 0 or 1,   wherein the sum of a+b=1 or 2.   
     
     
         2 . The oligonucleotide of  claim 1 , wherein the lipid is selected from the group consisting of 
       
         
           
           
               
               
           
         
       
     
     
         3 . The oligonucleotide of  claim 1 , wherein the polyethylene glycol has the following structure: 
       
         
           
           
               
               
           
         
         wherein n is 8 or 20. 
       
     
     
         4 . The oligonucleotide of  claim 1 , wherein X is selected from the group consisting of 
       
         
           
           
               
               
           
         
         wherein n is 8 or 20; and 
         wherein Y is 
       
       
         
           
           
               
               
           
         
       
     
     
         5 . The oligonucleotide of  claim 4 , wherein Q is a GPGO derived from an oncogene selected from the group consisting of c-Myc, c-Myb, VEGF, Bcl-2, K-ras, HIF-1α, Rb, RET, c-Kit, and PDGF-A. 
     
     
         6 . The oligonucleotide of  claim 5 , wherein Q is a c-Myc sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, and SEQ ID NO: 14; a is 1; and b is 0. 
     
     
         7 . The oligonucleotide of  claim 5 , wherein Q is a c-Myb sequence selected from the group consisting of SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, and SEQ ID NO: 20; a is 1; and b is 0. 
     
     
         8 . The oligonucleotide of  claim 5 , wherein Q is a VEGF sequence selected from the group consisting of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, and SEQ ID NO: 26;
 X is   
       
         
           
           
               
               
           
         
         a is 1; and b is 0. 
       
     
     
         9 . The oligonucleotide of  claim 5 , wherein Q is a K-ras sequence selected from the group consisting of SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, and SEQ ID NO: 35;
 X is selected from the group consisting of   
       
         
           
           
               
               
           
         
         a is 1; and b is 0. 
       
     
     
         10 . The oligonucleotide of  claim 5 , wherein Q is a RET sequence selected from the group consisting of SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 39, and SEQ ID NO: 40;
 X is selected from the group consisting of   
       
         
           
           
               
               
           
         
         wherein n is 8 or 20; a is 1; and b is 0. 
       
     
     
         11 . The oligonucleotide of  claim 5 , wherein Q is a HIF-1α sequence selected from the group consisting of SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, and SEQ ID NO: 47;
 X is 
 
       
         
           
           
               
               
           
         
       
       a is 1; and b is 0. 
     
     
         12 . The oligonucleotide of  claim 5 , wherein Q is a PDGF-A sequence selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, and SEQ ID NO: 55;
 X is   
       
         
           
           
               
               
           
         
       
       a is 1; and b is 0. 
     
     
         13 . The oligonucleotide of  claim 5 , wherein Q is a Bcl-2 sequence selected from the group consisting of SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, and SEQ ID NO: 65;
 X is selected from the group consisting of   
       
         
           
           
               
               
           
         
       
       a is 1; and b is 0. 
     
     
         14 . The oligonucleotide of  claim 5 , wherein Q is a c-Kit sequence selected from the group consisting of SEQ ID NOs: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, and SEQ ID NO: 70;
 X is   
       
         
           
           
               
               
           
         
       
       a is 1; and b is 0. 
     
     
         15 . The oligonucleotide of  claim 5 , wherein Q is a sequence selected from the group consisting of SEQ ID NOs: 1-70; a is 0; and b is 1. 
     
     
         16 . A composition comprising:
 (i) a safe and effective amount of an oligonucleotide according to the following Formula I:
   5′-X a -Q-Y b -3′   Formula I
 
 wherein: 
 X and Y are each independently selected from the group consisting of a lipid and a polyethylene glycol; 
 Q is a quadruplex-forming guanine-rich promoter gene oligonucleotide (GPGO); 
 a is 0 or 1; and 
 b is 0 or 1, 
   wherein the sum of a+b=1 or 2; and   (ii) a carrier,   wherein the oligonucleotide forms at least one quadruplex.   
     
     
         17 . A method of inhibiting cell growth comprising contacting a cell with the composition according to  claim 16 . 
     
     
         18 . A method of treating cancer comprising administering to a patient in need thereof the composition according to  claim 16 . 
     
     
         19 . The method of  claim 18 , wherein the cancer is a cancer that expresses an oncogene selected from the group consisting of c-Myc, c-Myb, VEGF, Bcl-2, K-ras, HIF-1α, Rb, RET, c-Kit, and PDGF-A. 
     
     
         20 . The method of  claim 18 , wherein the composition is administered orally, rectally, parenterally, intracistemally, intravaginally, intraperitoneally, intravesically, locally, or as a buccal or nasal spray. 
     
     
         21 . A method of treating a patient having a tumor, the method comprising:
 (a) performing a biopsy on the tumor;   (b) determining a gene expression profile of the tumor;   (c) identifying one or more oncogenes that are overexpressed in the tumor, based on the gene expression profile of step (b);   (d) administering to the patient a composition according to  claim 16 , wherein Q is a GPGO derived from the one or more overexpressed oncogenes identified in step (c).   
     
     
         22 . The method of  claim 21 , wherein Q is a GPGO derived from an oncogene selected from the group consisting of c-Myc, c-Myb, VEGF, Bcl-2, K-ras, HIF-1α, Rb, RET, c-Kit, and PDGF-A. 
     
     
         23 . The method of  claim 22 , wherein Q is a sequence selected from the group consisting of SEQ ID NOs: 1-70.